Methods and apparatus for measuring analytes using large scale FET arrays

Abstract

Methods and apparatus relating to very large scale FET arrays for analyte measurements. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. In one example, chemFET arrays facilitate DNA sequencing techniques based on monitoring changes in hydrogen ion concentration (pH), changes in other analyte concentration, and/or binding events associated with chemical processes relating to DNA synthesis.

What is claimed: 
     
       1. A method for using a semiconductor device, comprising:
 loading a microwell array with a sample of template nucleic acid-containing beads; the microwell array formed over a chemically-sensitive field effect transistor (chemFET) sensor array comprising at least 10 7  chemFET sensors, wherein each microwell of the microwell array corresponds to at least one chemFET sensor of the chemFET sensor array; 
 controlling a sequential flow of nucleotide reagents over the microwell array; 
 coupling circuitry to the chemFET sensor array to generate an output signal occurring for each sensor in the chemFET sensor array in response to release of an analyte resulting from incorporation of a nucleotide; and 
 analyzing output signals generated by the circuitry to determine a sequence corresponding to the template nucleic acid-containing beads. 
 
     
     
       2. The method of  claim 1 , wherein analyzing output signals includes determining a number of sequential nucleotide bases from a magnitude of the output signal. 
     
     
       3. The method of  claim 2 , wherein the output signal is a voltage signal. 
     
     
       4. The method of  claim 3 , wherein the voltage signal is output over a range of about 0 volts to about 2 volts. 
     
     
       5. The method of  claim 1 , wherein the output signal is in response to release of hydrogen ions resulting from incorporation of a nucleotide. 
     
     
       6. The method of  claim 5 , wherein the output signal is over a pH range between pH 6 to pH 9. 
     
     
       7. The method of  claim 1 , wherein the output signal is in response to release of pyrophosphate ions resulting from incorporation of a nucleotide. 
     
     
       8. The method of  claim 1 , wherein the output signal is in response to release of phosphate ions resulting from incorporation of a nucleotide. 
     
     
       9. The method of  claim 1 , wherein preparing the sample of template nucleic acid-containing beads includes incubating the beads with a sequencing primer and a polymerase. 
     
     
       10. The method of  claim 9 , further including selecting incubation conditions to provide that each template nucleic acid is hybridized to the sequencing primer and bound to the polymerase. 
     
     
       11. The method of  claim 1 , wherein the chemFET sensor array is mounted in a flow cell and controlling the sequential flow of nucleotide reagents over the microwell array comprises controlling the sequential flow of nucleotide reagents through the flow cell. 
     
     
       12. The method of  claim 11 , wherein before controlling the sequential flow of nucleotide reagents, the method further comprises:
 providing a stable reference potential for an output voltage of each chemFET sensor of the semiconductor device using a reference electrode in fluid communication with the flow cell. 
 
     
     
       13. The method of  claim 12 , wherein controlling the sequential flow of nucleotide reagents through the flow cell comprises using a fluid delivery system providing automated control of fluid delivery. 
     
     
       14. The method of  claim 13 , wherein using the fluid delivery system providing automated control of fluid delivery comprises providing automated control of valving. 
     
     
       15. The method of  claim 1 , wherein coupling circuitry to the chemFET sensor array to generate an output signal occurring for each sensor comprises:
 coupling a first column bias/readout circuit to a first group of sensors for receiving column output signals from the first group of sensors; and 
 coupling a second column bias/readout circuit to a second group of sensors for receiving column output signals from the second group of sensors. 
 
     
     
       16. The method of  claim 15 , wherein the first group of sensors and the second group of sensors are a first half of sensors and a second half of sensors of the chemFET sensor array.